Cancer is just one simple metaphor that explains the kinds of sorts of limitations the Shivans will put up with until they'll try to clean up whatever is seemingly causing apparent trouble. Local anima like Ken might be overreaching for the sake of humanity, for example.
I read that "TERMINATE" line in multiple ways. It could mean that a global command was terminated by a local anima like Ken. Or it could mean that the message itself was terminated because it revealed too much information. In this second case, it could be because it was very dangerous for the sanity of the human reader, or it was just too vital an info to be revealed to Laporte. Or the sneaking was spotted and "terminated".
The noosphere subversion bit is interesting, because it might be about either a possible Shambhala noosphere in the near future, or about Ken's own small noosphere, or it could also be about (more likely) Al'Dawa's own noosphere being subverted or in danger. From either the Shivans themselves or another phenomena related to GD. Either this info is being terminated or the process itself. However, in the mission itself, Laporte is continuously "hacked" through different set pieces and experiences after this point.